weights

Calculate weights for phylogenetic tree

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    Syntax

    W = weights(Tree)

    Description

    W = weights(Tree) calculates branch proportional weights for every leaf in Tree using the Thompson-Higgins-Gibson method. The distance of every segment of the tree is adjusted by dividing it by the number of leaves it contains. The sequence weights are the result of normalizing to unity the new patristic distances between every leaf and the root.

    example

    Examples

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    Open Live Script

    Create an ultrametric tree with specified branch distances.

    bd = [1 2 3]';
tr_1 = phytree([1 2;3 4;5 6],bd)
        Phylogenetic tree object with 4 leaves (3 branches)

    View the tree.

    view(tr_1)

    Figure Phylogenetic Tree 1 contains an axes object and other objects of type uigridlayout, uimenu. The axes object contains 13 objects of type line. One or more of the lines displays its values using only markers

    Display the calculated weights.

    weights(tr_1)
    ans = 4×1

    0.8000
    0.8000
    1.0000
    1.0000

    Input Arguments

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    Phylogenetic tree, specified as a phytree object.

    Output Arguments

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    Weights, returned as a vector.

    References

    [1] Thompson J.D., D.G. Higgins, and T.J. Gibson. "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Research 22, no. 22 (1994): 4673-4680.

    [2] Henikoff S., and J.G. Henikoff (1994). "Position-based sequence weights". Journal Molecular Biology 243, no. 4 (1994): 574-578.

    Version History

    Introduced in R2006a

    See Also

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